viewTargetAlignment: viewTargetAlignment

In ETHZ-INS/scanMiR: scanMiR

viewTargetAlignment

Description

viewTargetAlignment

Usage

viewTargetAlignment(
  m,
  miRNA,
  seqs = NULL,
  flagBulgeMatches = FALSE,
  p3.params = list(),
  min3pMatch = 3L,
  hideSingletons = FALSE,
  UGsub = TRUE,
  ...,
  outputType = c("print", "data.frame", "plot", "ggplot")
)

Arguments

m	A GRanges of length 1 giving the information for a given match, as produced by findSeedMatches.
miRNA	A miRNA sequence, or a KdModel object of the miRNA corresponding to the match in 'm'; alternatively, a KdModelList including the model.
seqs	The sequences corresponding to the seqnames of 'm'. Not needed if 'm' contains the target sequences.
flagBulgeMatches	Logical; whether to flag matches inside the bulge (default FALSE)
p3.params	See findSeedMatches.
min3pMatch	The minimum 3' alignment for any to be plotted
hideSingletons	Logical; whether to hide isolated single base-pair matches
UGsub	Logical; whether to show U-G matches
...	Passed to 'text' if 'outputType="plot"'.
outputType	Either 'print' (default, prints to console), 'data.frame', or 'plot'.

Value

Returns nothing 'outputType="print"'. If 'outputType="data.frame"', returns a data.frame containing the alignment strings; if 'outputType="ggplot"' returns a 'ggplot' object.

Examples

data(SampleKdModel)
seq <- c(seq1="CGACCCCTATCACGTCCGCAGCATTAAAT")
m <- findSeedMatches(seq, SampleKdModel, verbose=FALSE)
viewTargetAlignment(m, miRNA=SampleKdModel, seqs=seq)

ETHZ-INS/scanMiR documentation built on April 16, 2024, noon